Long noncoding RNAs in respiratory viruses: A review.

Long noncoding RNAs (lncRNAs) are defined as RNA molecules longer than 200 nucleotides that can regulate gene expression at the transcriptional or post-transcriptional levels. Both human lncRNAs and lncRNAs encoded by viruses can modulate the expression of host genes which are critical for viral replication, latency, activation of signalling pathways, cytokine and chemokine production, RNAi processing, expression of interferons (IFNs) and interferon-stimulated genes (ISGs). Studies on lncRNAs as key regulators of host-virus interactions may give new insights into therapeutic strategies for the treatment of related diseases. This current review focuses on the role of lncRNAs, and their interactions with respiratory viruses including influenza A virus (IAV), respiratory syncytial virus (RSV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Interplay between cellular metabolism and DNA viruses.

Viruses as intracellular pathogens take over the host metabolism and reprogram to facilitate optimal virus production. DNA viruses can cause alterations in several metabolic pathways, including aerobic glycolysis also known as the Warburg effect, pentose phosphate pathway activation, and amino acid catabolism such as glutaminolysis, nucleotide biosynthesis, lipid metabolism, and amino acid biosynthesis. The available energy for productive infection can be increased in infected cells via modification of different carbon source utilization. This review discusses the metabolic alterations of the DNA viruses that will be the basis for future novel therapeutic approaches.

In silico prediction of T-cell and B-cell epitopes of human papillomavirus type 16 L1 protein.

Human papillomavirus type 16 (HPV-16) is one of the most important cause of developing cervical cancer. Therefore, effective epitope-based vaccine design for HPV-16 would be of major medical benefit. The aim of our study was to identify B- and T-cell epitopes of HPV-16 L1 protein. In this study, the HPV-16 L1 gene was isolated from HPV recovered from five vaginal swab samples using specific primers and finally sequenced. The ExPASy translate tool (http://web.expasy.org/translate/) was used to convert nucleotide sequence into amino acid sequence. Bioinformatic analysis was employed to predict suitable B- and T-cell epitopes and immunogenicity, allergenicity, and toxicity of predicted epitopes were then evaluated. Afterward, the selected T-cell epitopes were docked using Molegro Virtual Docker software. The two epitopes 207 AMDFTTLQA215 and 200 MVDTGFGAM208 have showed a very strong binding affinity to HLA-A0201 and HLA-B3501 molecules, respectively. Outcome of B-cell epitope prediction showed that epitope 475 KAKPKFTLGKRK ATPTTSSTSTTAKRKK502 contained overlapped epitope, which might be the epitope associated with the production of neutralizing antibody response. Based on this finding, the predicted B- and T-cell epitopes are promising targets for epitope-based vaccine development against HPV-16. Further in vivo and in vitro experiments are needed to confirm our findings.

Interactions between SARS coronavirus 2 papain-like protease and immune system: A potential drug target for the treatment of COVID-19.

Coronaviruses (CoVs) are a large family of respiratory viruses which can cause mild to moderate upper respiratory tract infections. Recently, new coronavirus named as Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been identified which is a major threat to public health. Innate immune responses play a vital role in a host's defence against viruses. Interestingly, CoVs have evolved elaborate strategies to evade the complex system of sensors and signalling molecules to suppress host immunity. SARS-CoV-2 papain-like protease (PLpro), as an important coronavirus enzyme, regulates viral spread and innate immune responses. SCoV-2 PLpro is multifunctional enzyme with deubiquitinating (DUB) and deISGylating activity. The PLpro can interact with key regulators in signalling pathways such as STING, NF-κB, cytokine production, MAPK and TGF-ß and hijack those to block the immune responses. Therefore, the PLpro can be as an important target for the treatment of COVID-19. Until now, several drugs or compounds have been identified that can inhibit PLpro activity. Here we discuss about the dysregulation effects of PLpro on immune system and drugs that have potential inhibitors for SCoV-2 PLpro.

Complexity on modulation of NF-κB pathways by hepatitis B and C: A double-edged sword in hepatocarcinogenesis.

Nuclear factor-κB (NF-κB), a family of master regulated dimeric transcription factors, signaling transduction pathways are active players in the cell signaling that control vital cellular processes, including cell growth, proliferation, differentiation, apoptosis, morphogenesis, angiogenesis, and immune responses. Nevertheless, aberrant regulation of the NF-κB signaling pathways has been associated with a significant number of human cancers. In fact, NF-κB acts as a double-edged sword in the vital cellular processes and carcinogenesis. This review provides an overview on the modulation of the NF-κB signaling pathways by proteins of hepatitis B and C viruses. One of the major NF-κB events that are modulated by these viruses is the induction of hepatocellular carcinoma. Given the central function of NF-κB in carcinogenesis, it has turned out to be a considerable therapeutic target for cancer therapy.

Modulation of the immune response by Middle East respiratory syndrome coronavirus.

Coronavirus (CoV) infections are commonly associated with respiratory and enteric disease in humans and animals. In 2012, a new human disease called Middle East respiratory syndrome (MERS) emerged in the Middle East. MERS was caused by a virus that was originally called human coronavirus-Erasmus Medical Center/2012 but was later renamed as Middle East respiratory syndrome coronavirus (MERS-CoV). MERS-CoV causes high fever, cough, acute respiratory tract infection, and multiorgan dysfunction that may eventually lead to the death of the infected individuals. The exact origin of MERS-CoV remains unknown, but the transmission pattern and evidence from virological studies suggest that dromedary camels are the major reservoir host, from which human infections may sporadically occur through the zoonotic transmission. Human to human transmission also occurs in healthcare facilities and communities. Recent studies on Middle Eastern respiratory continue to highlight the need for further understanding the virus-host interactions that govern disease severity and infection outcome. In this review, we have highlighted the major mechanisms of immune evasion strategies of MERS-CoV. We have demonstrated that M, 4a, 4b proteins and Plppro of MERS-CoV inhibit the type I interferon (IFN) and nuclear factor-κB signaling pathways and therefore facilitate innate immune evasion. In addition, nonstructural protein 4a (NSP4a), NSP4b, and NSP15 inhibit double-stranded RNA sensors. Therefore, the mentioned proteins limit early induction of IFN and cause rapid apoptosis of macrophages. MERS-CoV strongly inhibits the activation of T cells with downregulation of antigen presentation. In addition, uncontrolled secretion of interferon É£-induced protein 10 and monocyte chemoattractant protein-1 can suppress proliferation of human myeloid progenitor cells.

Understanding lactate in the development of Hepatitis B virus-related hepatocellular carcinoma.

Hepatitis B Virus (HBV) is a hepatotropic virus that can establish a persistent and chronic infection in humans. Chronic hepatitis B (CHB) infection is associated with an increased risk of hepatic decompensation, cirrhosis, and hepatocellular carcinoma (HCC). Lactate level, as the end product of glycolysis, plays a substantial role in metabolism beyond energy production. Emerging studies indicate that lactate is linked to patient mortality rates, and HBV increases overall glucose consumption and lactate production in hepatocytes. Excessive lactate plays a role in regulating the tumor microenvironment (TME), immune cell function, autophagy, and epigenetic reprogramming. The purpose of this review is to gather and summarize the existing knowledge of the lactate's functions in the dysregulation of the immune system, which can play a crucial role in the development of HBV-related HCC. Therefore, it is reasonable to hypothesize that lactate with intriguing functions can be considered an immunomodulatory metabolite in immunotherapy.

Small extracellular vesicles as key players in cancer development caused by human oncogenic viruses.

BACKGROUND: Exosomes are the smallest group of extracellular vesicles in size from 30 to 150 nm, surrounded by a lipid bilayer membrane, and originate from multivesicular bodies secreted by different types of cells, such as virus-infected cells. The critical role of exosomes is information transfer among cells, representing a unique way for intercellular communication via a load of many kinds of molecules, including various signaling proteins and nucleic acids. In this review, we aimed to comprehensively investigate the role of exosomes in promoting human oncogenic viruses-associated cancers. METHODS: Our search was conducted for published researches between 2000 and 2022 by using several international databases includeing Scopus, PubMed, and Web of Science as well as Google scholar. We also reviewed additional evidence from relevant published articles. RESULTS: It has been shown that exosomes can create the conditions for viral spread in viral infections. Exosome secretion in a human tumor virus can switch on the cell signaling pathways by transferring exosome-encapsulated molecules, including viral oncoproteins, signal transduction molecules, and virus-encoded miRNAs, into various cells. CONCLUSION: Given the role of exosomes in viruses-associated cancers, they can also be considered as molecular targets in diagnosis and treatment.

Designing of DNA Vaccine Based on a Secretory Form of Major Capsid Protein of Human Papillomavirus Type 18.

More than 99% of cervical cancers are associated with human papillomaviruses (HPVs) worldwide. Current HPV vaccines are safe, highly immunogenic, with effective immunity against specific HPV types. However, DNA vaccines are a new appealing platform which can be considered for designing the HPV vaccines. This study aimed to construct a recombinant eukaryotic expression plasmid containing L1 of HPV-18, tissue plasminogen activators (tPA), and pan HLA DR-binding epitope (PADRE) genes into the pVAX1 vector. The L1, tPA, and PADRE genes were amplified in a thermocycler. The polymerase chain reaction (PCR) products were cloned and insertion of the genes was confirmed using colony PCR, restriction enzymes analysis, and sequencing methods. Indirect immunofluorescence, RT-PCR, and western blot assays were applied to identify the target gene in HEK-293 cells. Total IgG and its isotypes in immunized mice were measured by enzyme-linked immunosorbent assay technique. Western blot analysis showed a protein band of about 67.5 kDa in supernatant and cell lysate of transfected cells. The results of mice immunization with different constructs (group 1: the pVAX-L1, group 2: pVAX-tPA-PADRE-L1, group 3: pVAX1, and group 4: PBS as controls) indicated that the pVAX1-tPA-PADRE-L1 construct induced a significantly higher level of total IgG than pVAX1-L1 (p=0.003). In conclusion, pVAX1-tPA-PADRE-L1 recombinant plasmid is a highly immunogenic construct and suggests as a promising candidate for vaccine development against HPV type 18 in low-middle-income countries.

Seronegative occult hepatitis C infection among hemodialysis patients: A prevalence study.

The aim of this study was to investigate the prevalence of occult hepatitis C virus (HCV) infection (OCI) among HD patients. Blood samples were taken from 79 HD patients and their sera were evaluated for the presence of anti-HCV. Both the sera and peripheral blood mononuclear cells (PBMCs) were then checked for HCV RNA by nested reverse transcriptase-polymerase chain reaction. Anti-HCV was positive among 4/79 (5.1%) of the patients. From 75 patients who were negative for anti-HCV, 71 (94.7%) patients were also negative for HCV RNA in sera samples but five of them were positive for HCV RNA in PBMCs. Totally, out of 79 patients, HCV RNA was detected in PBMCs of five (6.3%) patients, indicating that these patients had OCI. No significant difference was observed between the frequency of OCI and gender (P-value = .6). HCV genotype in all five cases of OCI was genotype 3a. Our study showed prevalence rate of 6.3% OCI infection in HD patients. Regarding the serious complications and the clinical importance of OCI in HD patients, sensitive diagnostic methods for identifying HCV RNA in the PBMCs should be implemented for all HD patients.

Hepatitis C virus core protein modulates several signaling pathways involved in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is the fifth most common cancer, and hepatitis C virus (HCV) infection plays a major role in HCC development. The molecular mechanisms by which HCV infection leads to HCC are varied. HCV core protein is an important risk factor in HCV-associated liver pathogenesis and can modulate several signaling pathways involved in cell cycle regulation, cell growth promotion, cell proliferation, apoptosis, oxidative stress and lipid metabolism. The dysregulation of signaling pathways such as transforming growth factor ß (TGF-ß), vascular endothelial growth factor (VEGF), Wnt/ß-catenin (WNT), cyclooxygenase-2 (COX-2) and peroxisome proliferator-activated receptor α (PPARα) by HCV core protein is implicated in the development of HCC. Therefore, it has been suggested that this protein be considered a favorable target for further studies in the development of HCC. In addition, considering the axial role of these signaling pathways in HCC, they are considered druggable targets for cancer therapy. Therefore, using strategies to limit the dysregulation effects of core protein on these signaling pathways seems necessary to prevent HCV-related HCC.

Evaluation of the thermal stability of live-attenuated Rubella vaccine (Takahashi strain) formulated and lyophilized in different stabilizers.

Live attenuated viral vaccines are difficult to handle and often sensitive to temperature. The viral titer may drop during the processing and storing stage, especially at high temperatures. Using live attenuated viral vaccines successfully depends on keeping the sufficient potency required for an immune response. Although freeze-drying makes the vaccine more stable, in the absence of appropriate stabilizer the process may affect the structure and viability of the viruses. Therefore, the formulation of vaccine by means of an appropriate stabilizer plays a crucial role in the stability of viral structure and potency of the vaccine. This study aimed to evaluate the effect of two new stabilizers, including a Trehalose-based stabilizer (T) and a stabilizer containing sucrose, human serum albumin and sorbitol (S) on the thermal stability of lyophilized live-attenuated Rubella virus (Takahashi strain). Two Rubella vaccines were formulated using different stabilizers and were lyophilized. The potency of produced vaccines was investigated using accelerated stability test. To determine the pattern of thermal stability of reconstituted vaccines in 24 h, incubating at three different temperatures and continuous sampling was also included in this study. The viral titer was calculated by TCID50 method. The regression analysis revealed that T vaccine found the sufficient stability compared to commercial Rubella vaccine containing a gelatin-based (G) stabilizer.

The frequency of Epstein-Barr virus among hemodialysis patients, Ahvaz, Iran.

BACKGROUND AND OBJECTIVES: Epstein-Barr virus (EBV) has infected more than 90% of adults worldwide. EBV infection is asymptomatic in healthy individuals and is controlled by a robust immune response while in individuals with weakened immunesystems including Hemodialysis (HD) patients and transplant recipients leads to serious illnesses. This study was aimed to investigate the frequency of EBV among the HD patients. MATERIALS AND METHODS: The cross-sectional study was carried out on 84 HD patients. These sera were checked for anti-EBV (VCA) IgG Ab assessment using enzyme-linked immunosorbent assay (ELISA). The DNA was extracted from the sera samples and tested for EBV DNA using nested PCR. RESULTS: 52/84 (61.9%) of HD were males and 32/84 (38.1%) were females. The average age of participants was varying from 18 to 85 years while the mean age was 52 ± 1.57 SD years. 81 of 84 (96.42%); including 49/52 (94.23%) male and 32/32 (100%) female, were positive for anti-EBV (VCA) IgG antibody while 3 (3.58%) were negative. No significant differences were observed between the subjects regarding gender (P=0.28). EBV DNA was detected in 7 (8.33%) individuals, including 6 (11.53%) and 1 (3.12%) in male and female, respectively (P=0.24). CONCLUSION: Our study results showed that high prevalence of anti-EBV (VCA) IgG antibody (96.42%) were observed among the HD patients. Although the status of EBV latency was not performed, but it seems many of these patients are at risk of EBV-reactivation during the organ transplantation. As a result, it is recommended that the detection of EBNA-1 gene as a marker of EBV latency should be implemented for all HD patients to prevent EBV reactivation during organ transplantation.

Dominance of Variant Human Herpesvirus 6 A Among Hemodialysis Patients, Ahvaz, Iran.

INTRODUCTION: Hemodialysis (HD) patients are a high-risk population for acquiring blood-borne viruses such as HHV-6. HHV-6 can remain latent in the host cells after primary infection; the reactivation of virus may result complications such as seizure, respiratory failure, hepatitis, and encephalitis. There is a limited report concerning HHV-6 infection in HD patients in Iran. Thus, this study was conducted to determine the frequency of HHV-6 among HD patients. METHODS: We determined HHV-6 DNA in sera samples of 84 patients undergoing HD. The DNA was extracted from the sera samples and the presence of HHV-6 DNA variants A and B was evaluated by nested PCR. RESULTS: 52/84 (61.9%) of HD patients were males and 32/84 (38.1%) females. The age ranges of patients were between 18 to 85 years and the mean age was 52 ± 1.52 (± SD) years. Out of 84 sera samples, HHV-6 DNA was detected in 10 (11.9%) participants, including 6/52 (11.5%) in males and 4/32 (12.5%) in females. HHV- 6A was detected in 10/10 (100%) of positive cases. No HHV-6 B was found in HD patients. The distribution of HHV-6A DNA was not significant between genders (P > .05). Out of 84 HD patients, 55 (65.47%) cases were over 50 years, among them 10 (18.18%) cases were positive for HHV-6 A infection (P < .05). CONCLUSION: The results showed that only HHV-6 DNA variant A was found in 11.9% of HD patients. Regarding the consequence of HHV-6 reactivation, to manage and improve treatment, the screening of HHV-6 DNA test should be implemented for HD patients.

The Evaluation of Nerve Growth Factor Over Expression on Neural Lineage Specific Genes in Human Mesenchymal Stem Cells.

OBJECTIVE: Treatment and repair of neurodegenerative diseases such as brain tumors, spinal cord injuries, and functional disorders, including Alzheimer's disease, are challenging problems. A common treatment approach for such disorders involves the use of mesenchymal stem cells (MSCs) as an alternative cell source to replace injured cells. However, use of these cells in hosts may potentially cause adverse outcomes such as tumorigenesis and uncontrolled differentiation. In attempt to generate mesenchymal derived neural cells, we have infected MSCs with recombinant lentiviruses that expressed nerve growth factor (NGF) and assessed their neural lineage genes. MATERIALS AND METHODS: In this experimental study, we cloned the NGF gene sequence into a helper dependent lentiviral vector that contained the green fluorescent protein (GFP) gene. The recombinant vector was amplified in DH5 bacterial cells. Recombinant viruses were generated in the human embryonic kidney 293 (HEK-293) packaging cell line with the helper vectors and analyzed under fluorescent microscopy. Bone marrow mesenchymal cells were infected by recombinant viruses for three days followed by assessment of neural differentiation. We evaluated expression of NGF through measurement of the NGF protein in culture medium by ELISA; neural specific genes were quantified by real-time polymerase chain reaction (PCR). RESULTS: We observed neural morphological changes after three days. Quantitative PCR showed that expressions of NESTIN, glial derived neurotrophic factor (GDNF), glial fibrillary acidic protein (GFAP) and Microtubule-associated protein 2 (MAP2) genes increased following induction of NGF overexpression, whereas expressions of endogenous NGF and brain derived neural growth factor (BDNF) genes reduced. CONCLUSION: Ectopic expression of NGF can induce neurogenesis in MSCs. Direct injection of MSCs may cause tumorigenesis and an undesirable outcome. Therefore an alternative choice to overcome this obstacle may be the utilization of differentiated neural stem cells.